New approaches for assembly of short-read metagenomic data
New approaches for assembly of short-read metagenomic data
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DOI：
10.7287/peerj.preprints.27332v1
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发表时间：
2018-11
期刊：
影响因子：
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通讯作者：
Martin Ayling;M. Clark;R. Leggett
中科院分区：
文献类型：
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作者：
Martin Ayling;M. Clark;R. Leggett
近年来，结合组装算法的进步，使用更长范围的读取数据已经刺激了基因组组装的连续性和质量的巨大改善。然而，这些进展并没有直接转移到宏基因组数据集，因为当以不同丰度水平组装多个基因组时，单基因组组装算法所做的假设并不适用。宏基因组数据专用汇编器的开发是一个相对较晚的创新，多年来，研究人员不得不使用为单个基因组设计的工具。在过去的几年里，这种情况发生了变化，我们看到了一种使用不同原理构建的新型工具的出现。在这篇综述中，我们描述了宏基因组组装中固有的挑战，并比较了这些新的组装工具所采取的不同方法。
In recent years, the use of longer-range read data combined with advances in assembly algorithms has stimulated big improvements in the contiguity and quality of genome assemblies. However, these advances have not directly transferred to metagenomic datasets, as assumptions made by the single genome assembly algorithms do not apply when assembling multiple genomes at varying levels of abundance. The development of dedicated assemblers for metagenomic data was a relatively late innovation and for many years, researchers had to make do using tools designed for single genomes. This has changed in the last few years and we have seen the emergence of a new type of tool built using different principles. In this review, we describe the challenges inherent in metagenomic assemblies and compare the different approaches taken by these novel assembly tools.